RGT - Regulatory Genomics Toolbox

RGT is an open source Python 3.6+ library for analysis of regulatory genomics. RGT is programmed in an oriented object fashion and its core classes provide functionality for handling regulatory genomics data.

The toolbox is made of a core library and several tools:

• HINT: ATAC-seq/DNase-seq footprinting method
• THOR: ChIP-Seq differential peak caller
• Motif Analysis: TBFS match and enrichment
• RGT-Viz: Visualization tool
• TDF: DNA/RNA triplex domain finder

See https://reg-gen.readthedocs.io for documentation and tutorials.

Installation

The quickest and easiest way to get RGT is to to use pip. First some dependencies:

pip install --user cython numpy scipy

Then install the full RGT suite with all other dependencies:

pip install --user RGT

Detailed installation instructions and basic problem solving can be found on our website.